Implemented support for reference genomes compressed with the BGZIP a…

[PSB-mibel]

…lgorithm. Implementation was derived from the GMOD-bgzf package, and reimplemented to make use of the igvxhr interface. To make use of the compression, simply add the compressedIndexURL parameter to the reference object that is provided to igv.js. Important note: the current implementation only works when the reference genome is indexed! Compressed by non-indexed genomes are currently not supported.

As indicated in issue #864 I've mostly made use of the work from the @GMOD team (https://github.com/GMOD/).
As both projects (IGV.js and GMOD) are released under the MIT license, I think licensing wise this copying/deriving of code should be fine.

I've tried following the coding style from the original file (e.g. no semicolons etc.), and in the end I didn't need to use any additional packages, so building the project using Rollup should work fine.

If there's any issues related to this patch, feel free to contact me: mibel@psb.ugent.be

[jrobinso]

@PSB-mibel Thanks this will be appreciated by many. I will merge it as soon as I'm able.

[jrobinso]

Apologies for the delay on this, I had some unexpected interruptions and then a lot of IGV desktop issues to work through. This is now my priority for the rest of the week.

[jrobinso]

@PSB-mibel this is merged. And BTW this was a very nice PR, existing code was touched minimally and it was very easy to review. Not all are like that, thanks. I have added a unit test which I will push shortly.

[PSB-mibel]

Thanks for the compliment. I hope the changes pass the unit test.
I've already deployed my build of IGV.js with support for the bgzip ref genome, and everything does seem to be working fine up until now, so I don't expect the unit test to fail. However, if it does, I'll be happy to try and help debug it.

[jrobinso]

Its working, already merged to master. This will be in the next release.